Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1269 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0619155361 sf0619154364 6 19155361 2.70E-09 2.50E-06
vg0619157347 sf0619156350 6 19157347 3.92E-09 2.07E-06
vg0920389319 sf0920388838 9 20389319 3.35E-08 NA
vg0810647541 sf0810646545 8 10647541 1.69E-07 1.69E-06
vg0619405763 sf0619404766 6 19405763 2.68E-07 3.22E-06
vg0419763927 sf0419591962 4 19763927 3.53E-06 2.02E-06